Bioinformatics and Computational Biology Core

Overview

The Bioinformatics and Computational Biology Core provides advanced data analysis and computational support to investigators at the Hackensack Meridian Health Center for Discovery and Innovation and collaborating institutions. The Core enables researchers to extract meaningful insights from large and complex biological datasets generated through modern high-throughput technologies.

Our team collaborates closely with investigators to design analytical strategies, implement robust computational pipelines, and translate raw biological data into interpretable and publication-ready results. Services span genomics, transcriptomics, multi-omics integration, computational pathology, and advanced data science approaches.

Mission

The mission of the Bioinformatics and Computational Biology Core is to support cutting-edge biomedical research by providing state-of-the-art computational tools, expertise in data analysis, and collaborative scientific support. We aim to accelerate discovery by enabling investigators to efficiently interpret complex datasets and integrate computational insights into biological and clinical research.

Services and Capabilities

The Core provides a comprehensive suite of computational and analytical services supporting genomics, molecular biology, systems biology, and biomedical data science.

Next-Generation Sequencing (NGS) Data Analysis

Support for analysis of high-throughput sequencing datasets across a range of experimental platforms.

DNA Sequencing

• Whole-genome sequencing (WGS)
• Whole-exome sequencing (WES)
• Targeted sequencing panels
• Variant calling (SNVs, indels) and functional annotation
• Structural variant and copy number analysis

RNA Sequencing

• Differential gene expression analysis
• Transcript quantification and isoform detection
• Alternative splicing analysis
• Fusion gene detection

Epigenomics

• ChIP-seq analysis for transcription factor binding and histone modifications
• DNA methylation analysis
• Methyl-seq, nanoNOME-seq, and QDNAseq workflows

Single-Cell and Spatial Omics

• Single-cell RNA-seq (scRNA-seq) processing and quality control
• Dimensionality reduction, clustering, and cell-type identification
• Integration of multi-sample or multi-modal datasets

Amplicon Sequencing

• Barcode design and experimental planning
• Demultiplexing and deconvolution
• Analysis of lineage tracing and barcoding experiments

Structural Biology and Proteomics

Computational analysis supporting protein structure, function, and interaction studies.

• Protein functional annotation
• Structural visualization and modeling
• Molecular docking and protein–ligand interaction analysis
• Integration and analysis of proteomics datasets

Systems Biology and Evolutionary Analysis

Tools for understanding biological systems, microbial communities, and evolutionary processes.

• Metagenomic taxonomic and functional profiling
• Microbiome diversity analysis
• Phylogenetic tree reconstruction
• Ancestral sequence inference and evolutionary analysis
• Pathway enrichment analysis (GO terms, KEGG)

Data Science and Custom Computational Solutions

Advanced computational methods tailored to investigator needs.

• Machine learning for disease classification and biomarker discovery
• Predictive modeling for drug targets and biological outcomes
• Statistical modeling and biostatistical analysis
• Power analysis and experimental design support
• Custom pipeline development in Python and R
• Development of scientific software, analysis workflows, and interactive data visualization tools
• Design of non-coding oligonucleotides including diagnostic primers and CRISPR guide RNAs

Digital and Computational Pathology

Integration of computational image analysis with molecular data.

• Analysis of digitized pathology slides
• Tissue segmentation and classification
• Quantitative analysis of histology (H&E) and immunohistochemistry (IHC)
• Spatial transcriptomics and multiplexed imaging data analysis
• Detection and segmentation of cellular and tissue features

Operational Workflow

The Bioinformatics Core collaborates closely with investigators throughout the lifecycle of a project.

Project Request
Investigators submit a request through email or the CDI website.

Consultation
Core scientists meet with investigators to discuss experimental design, sequencing technologies, data requirements, and statistical considerations.

Project Proposal
A detailed scope of work (SOW), timeline, and cost estimate are provided.

Data Analysis
The Core performs data processing, quality control, and in-depth computational analysis.

Results Delivery
Investigators receive processed datasets, analytical reports, and publication-quality figures.

Fees and Access

The Bioinformatics and Computational Biology Core operates on a fee-for-service model.

• Costs vary depending on project scope and computational requirements
• Detailed cost estimates are provided prior to project initiation
• Projects are scheduled based on availability and project complexity

Billing is administered through CDI administrative services.
Payment mechanisms may include institutional accounts, grants, and purchase orders.

Investigator Support

In addition to data analysis services, the Core provides broader support for research programs.

Grant Support

• Letters of Support (LOS) for grant proposals
• Assistance with writing data analysis sections of grant applications

Training and Education

• Workshops and tutorials in bioinformatics and computational biology

Data Management

• Assistance with long-term data storage and archiving
• Support for submissions to public repositories (e.g., NCBI)
• Guidance on secure and compliant data management practices

Team

Core Leadership

Erika Shor, Ph.D.
Bioinformatics Core Lead
Member, CDI
Erika.shor@hmh-cdi.org

Computational Biology and Data Science Staff

Ariel Aptekmann, Ph.D.
Bioinformatician
ariel.aptekmann@hmh-cdi.org

Tara Lozy, MA – Biostatistician
Ziv Frankenstein, Ph.D. – Bioinformatician
Emilio Kolomensky, Ph.D. – Bioinformatics Consultant
Gustavo Levcovich – Software Development Consultan

CDI Faculty and Associated Experts

Additional CDI investigators contribute expertise in genomics, computational biology, and statistical analysis.

Alvin Makohon-Moore, Ph.D. – Barcoding, phylogenetics, cancer genomics
Andy Madrid, Ph.D. – Nanopore genomics and epigenomics
Austin Terlecky, BA/BS – Nanopore genomics and molecular microbiology
Jianping Jiang, Ph.D. – Nanopore genomics and microbial genomics
Benjamin Tycko, Ph.D. – Nanopore sequencing and epigenomics